PS: this does not work for very small atoms, e.g. waters. Here I let the temperature factor take care of the occupancy as well.
Von: Schreuder, Herman /DE Gesendet: Donnerstag, 3. März 2022 16:23 An: CCP4BB@JISCMAIL.AC.UK Betreff: AW: [ccp4bb] Ligand occupancy refinement Dear Ankanksha, The ligand is either present, or it is not present. It cannot be that some atoms are present and others not. For ligands, I always use a single group occupancy using the program Buster from global phasing. In my hands, this always works. There is a correlation between occupancy and B-factors, but if you use a single occupancy for a large number of atoms, this correlation is not longer a problem. Also, modern maximum likelihood refinement programs do a good job in separating the contributions of occupancy and B-factors. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Jon Cooper Gesendet: Donnerstag, 3. März 2022 16:09 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: Re: [ccp4bb] Ligand occupancy refinement Hello, the ligand needs to be treated as one occupancy group since refining individual occupancies would be a case of refining too many parameters, unless it was a very fragmentary compound!! It is one keyword in refmac, but I can't remember for phenix, sorry! Ta jc Sent from ProtonMail mobile -------- Original Message -------- On 3 Mar 2022, 14:15, Akanksha Tomar < akankshat...@gmail.com<mailto:akankshat...@gmail.com>> wrote: Hi everyone, I am trying to refine the occupancy of a bound ligand. After fixing the protein model and water I fitted the ligand into it. Currently, I am using Phenix Refine with occupancy refinement for individual atoms switched on. After the refinement, the overall occupancy of the ligand is 0.7 and the RSCC value is 0.86. The resolution of the structure is 2.1 Å. Now the problem is that the program has assigned different occupancies to different atoms of the ligand. For some cases, it has assigned 0 occupancies to atoms for which there is a clear positive peak. Why it has been done so and is it acceptable? Any help would be greatly appreciated. Thank you. -- Best Regards, Akanksha Tomar Pre-Doctoral Fellow, C\o Dr. Arockiasamy Arulandu, Membrane Protein Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, India ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
